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To address the noisy nature of dim lesions (at baseline), de Langen et al. [ 7] propose cut-off regions that depend both on minimum absolute %-change in SUVmax and a concomitant minimum absolute change in SUVmax (cf., their Table 2).
cSignificance defined as a minimum absolute change of 30% comparing exposure groups and a p-value < 0.05.
This is the minimum absolute change necessary for classification as a responder in the Osteoarthritis Research Society International OARS I) response criteria [ 32, 33].
In one epigenome-wide association study in the SMART study population (N = 35) [ 29], only one CpG site in the TSP50 gene promoter showed increased DNA methylation with elevated BPA exposure under the established significance threshold of minimum absolute change of 10% by BPA levels and a P value <0.05.
Sample size was calculated for the primary study outcome, using the following: where n = number of subjects per group, α = significance level (2-sided testing), 1 - β = power, σ = SD of change within individuals, ICC = intraclass correlation, m = average cluster size, Δ = minimum absolute change to be detected, number of clusters (therapists) = n/m.
In one epigenome-wide association study in the SMART study population (N = 43) [ 53], only two CpG sites in the GSTM1 gene showed increased DNA methylation with elevated blood mercury exposure under the established significance threshold of minimum absolute change of 10% and a P value <0.05.
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STEM parameters differing from default values were the following: "No normalization/add 0"; "Filtering Minimum absolute expression change = 0,20"; "Cluster profile Minimum correlation = 0,75".
For this clustering, those profiles that did not show a minimum absolute expression change of 4 log-fold (based on the difference between the minimum and maximum) were filtered out.
From the 42,430 total genes we selected for time-series analysis only those with a minimum absolute expression change between time-points of 4-fold resulting in a total of 2,095 genes.
As shown, the corrected p-values range from the lowest for profile 44 to the highest for profile 2. Table 2 summarizes the number of significantly deregulated transcripts across all time-points with respect to the two criteria of "Maximum Number of Missing Values" and "Minimum Absolute Expression Change (from Zero)".
For the DREM 2.0 analysis the following options were not set to default values: (i) genes in the time course were discarded if "Minimum Absolute Expression Change" was smaller than 0.5, (ii) "incorporate expression in regulator data" was activated for transcription factors with "Expression scaling weight" set to 1.
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minimum absolute average
minimum meaningful change
minimum absolute count
minimum absolute percent
minimum absolute abundance
minimum clinical change
minimum absolute size
minimum absolute intensity
minimum absolute difference
minimum absolute value
minimum absolute %-change
minimum absolute fold
minimum absolute t
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